The invention relates to a real-time fluorescence PCR (polymerase chain reaction) detection system based on a rotary type microfluidic chip. The system comprises an annealing low-temperature area, an extension appropriate temperature area, a thermal change high temperature area, a rotating module, a PCR reagent accommodating cavity, an injection micro-channel, an instrument fixing base and a fluorescence detection system, wherein a temperature cycle control module comprises the annealing low-temperature area, the extension appropriate temperature area and the thermal change high temperature area; a micro-channel cycle PCR amplification module comprises the rotating module, the PCR reagent accommodating cavity, the injection micro-channel and the instrument fixing base; and a fluorescence spectrum detection module comprises the fluorescence detection system. According to the system, three modules, namely, the micro-channel cycle PCR amplification module, the temperature cycle control module and the fluorescence spectrum detection module are integrated, so that the portable micro PCR fluorescence real-time detection system applicable to space operation requirements is realized, and purposes of function integration, structure microform, lightness, small size and full-automatic detection are achieved.